Potential threat of biological warfare agent (BWA) attacks as well as spread of SARS (Severe Acute Respiratory Syndrome) virus to more than two dozen countries and a recent threat of global spread of bird flu virus emphasized the need for urgent development of diagnostic systems which will be capable to rapidly recognize emergence of dangerous infectious diseases with potential epidemiologic consequences. Current DNA based portable systems for the detection of infectious agents lack multiplexing, i.e., simultaneous analysis of large number of pathogens or their genes, they do not integrate well or automate the sample preparation methods and cannot be used efficiently in the field or in point-of care applications. The microarray platform practically does not pose a limit to multiplexed detection of large number of pathogens as well as their characterization by multiple genes. The Phase I project successfully demonstrated several innovative approaches to sample preparation using centrifugal microfluidics. Three dimensional or multilayer centrifugal discs (3DCD) have been designed and fabricated which offer practically unlimited surface area for implementation of different sample preparation techniques. Several innovative tools for sample preparation in the 3DCD format have been demonstrated in the Phase I project. The overall goal of the Phase II project is to integrate these tools and develop CDs for particular assays for the detection of infectious disease and/or biological warfare agents. A DNA microarray detection platform will be integrated with the sample preparation on the 3DCD. An electronic microarray technology developed and commercialized earlier, will be used in detection. This technology assures fast DNA detection times using electrophoretically driven DNA transport and hybridization on the microarray. Specific aims of the Phase II program is to develop 3DCD technology with embedded tools for complete sample preparation and detection of several representative respiratory infectious disease pathogens as well as biological warfare agents. A fully developed technology will yield a small portable or point-of-care system with exchangeable CDs allowing choice of the pathogen detection panels including respiratory infectious disease, biological warfare agents or emergent viruses panels.